# this cell is tagged as parameters for `papermill` parameterization
binding_data = None
HENV103_filter = None
HENV117_filter = None
HENV26_filter = None
HENV32_filter = None
m102_filter = None
nAH1_filter = None

altair_config = None
nipah_config = None
escape_bubble_plot = None
bubble_1_mut_plot = None
mab_line_escape_plot = None
aggregate_mab_and_binding = None
aggregate_mab_and_niv_polymorphism = None
binding_vs_escape = None

mab_plot_top = None
mab_plot_all = None

# Parameters
nipah_config = "nipah_config.yaml"
altair_config = "data/custom_analyses_data/theme.py"
HENV103_filter = "results/filtered_data/HENV103_escape_filtered.csv"
HENV117_filter = "results/filtered_data/HENV117_escape_filtered.csv"
HENV26_filter = "results/filtered_data/HENV26_escape_filtered.csv"
HENV32_filter = "results/filtered_data/HENV32_escape_filtered.csv"
m102_filter = "results/filtered_data/m102_escape_filtered.csv"
nAH1_filter = "results/filtered_data/nAH1_escape_filtered.csv"
binding_data = "results/filtered_data/E2_binding_filtered.csv"
escape_bubble_plot = "results/images/escape_bubble_plot.html"
bubble_1_mut_plot = "results/images/escape_bubble_1_mut_plot.html"
overlap_escape_plot = "results/images/overlap_escape_plot.html"
mab_line_escape_plot = "results/images/mab_line_escape_plot.html"
mab_plot_top = "results/images/mab_plot_top.html"
mab_plot_all = "results/images/mab_plot_all.html"
aggregate_mab_and_binding = "results/images/aggregate_mab_and_binding.html"
binding_vs_escape = "results/images/binding_vs_escape.html"
aggregate_mab_and_niv_polymorphism = (
    "results/images/aggregate_mab_and_niv_polymorphism.html"
)

if binding_data is None:
    print("this is being run manually")
else:
    print("papermill!")

papermill!

import math
import os
import re

import altair as alt

import numpy as np

import pandas as pd

import scipy.stats

import Bio.SeqIO
import yaml
import matplotlib

matplotlib.rcParams["svg.fonttype"] = "none"

from Bio import PDB
import dmslogo
from dmslogo.colorschemes import CBPALETTE
from dmslogo.colorschemes import ValueToColorMap

# allow more rows for Altair
_ = alt.data_transformers.disable_max_rows()

if (
    os.getcwd()
    == "/fh/fast/bloom_j/computational_notebooks/blarsen/2023/Nipah_Malaysia_RBP_DMS/"
):
    pass
    print("Already in correct directory")
else:
    os.chdir(
        "/fh/fast/bloom_j/computational_notebooks/blarsen/2023/Nipah_Malaysia_RBP_DMS/"
    )
    print("Setup in correct directory")

Setup in correct directory

if binding_vs_escape is None:
    altair_config = "data/custom_analyses_data/theme.py"
    nipah_config = "nipah_config.yaml"

    binding_data = "results/filtered_data/E2_binding_filtered.csv"

    HENV103_filter = "results/filtered_data/HENV103_escape_filtered.csv"
    HENV117_filter = "results/filtered_data/HENV117_escape_filtered.csv"
    HENV26_filter = "results/filtered_data/HENV26_escape_filtered.csv"
    HENV32_filter = "results/filtered_data/HENV32_escape_filtered.csv"
    m102_filter = "results/filtered_data/m102_escape_filtered.csv"
    nAH1_filter = "results/filtered_data/nAH1_escape_filtered.csv"

    # escape_bubble_plot = 'results/images/escape_bubble_plot.html'
    # bubble_1_mut_plot = 'results/images/escape_bubble_1_mut_plot.html'
    # overlap_escape_plot = 'results/images/overlap_escape_plot.html'

    # m102_heat = 'results/images/m102_heatmap.html'
    # HENV26_heat = 'results/images/HENV26_heatmap.html'
    # HENV32_heat = 'results/images/HENV32_heatmap.html'
    # nAH1_heat = 'results/images/nAH1_heatmap.html'
    # HENV117_heat = 'results/images/HENV117_heatmap.html'
    # HENV103_heat = 'results/images/HENV103_heatmap.html'

if altair_config:
    with open(altair_config, "r") as file:
        exec(file.read())

with open(nipah_config) as f:
    config = yaml.safe_load(f)

# Make a dataframe with all the mutants with low entry scores for masking later in script
func_scores_E3 = pd.read_csv(
    "../Nipah_Malaysia_RBP_DMS/results/func_effects/averages/CHO_EFNB3_low_func_effects.csv"
)
func_scores_E3_low_effect = func_scores_E3[
    (func_scores_E3["effect"] < config["min_func_effect_for_ab"])
    & (func_scores_E3["times_seen"] > config["func_times_seen_cutoff"])
    & (func_scores_E3["site"] != 603)
    & (func_scores_E3["mutant"] != "-")
    & (func_scores_E3["mutant"] != "*")
]
display(func_scores_E3_low_effect)

HENV103 = pd.read_csv(HENV103_filter)
HENV117 = pd.read_csv(HENV117_filter)
HENV26 = pd.read_csv(HENV26_filter)
HENV32 = pd.read_csv(HENV32_filter)
m102 = pd.read_csv(m102_filter)
nAH1 = pd.read_csv(nAH1_filter)

# Combine all the individual filtered antibody escape files
combined_df = pd.concat([HENV103, HENV117, HENV26, HENV32, m102, nAH1])
combined_df = combined_df[
    [
        "site",
        "wildtype",
        "mutant",
        "mutation",
        "effect",
        "escape_median",
        "escape_std",
        "times_seen_ab",
        "show_site",
        "ab",
    ]
]
display(combined_df)

# Make a separate dataframe that only has the top sites
filtered_df = combined_df.query("show_site == True")
filtered_df = filtered_df[filtered_df["escape_median"] >= config["min_escape_cutoff"]]
display(filtered_df)

def identify_escape_sites(df, ab):
    subset = df[(df["ab"] == ab)]
    unique_sites = list(subset["site"].unique())
    return unique_sites


abs = ["HENV-26", "HENV-103", "HENV-32", "HENV-117", "m102.4", "nAH1.3"]
sites_dict = {}  # Create an empty dictionary to store the results

for ab in abs:
    sites_dict[ab] = identify_escape_sites(filtered_df, ab)

display(sites_dict)  # need site dict for later

{'HENV-26': [166, 171, 204, 257, 490, 491, 492, 494, 497, 501, 529, 530],
 'HENV-103': [154, 176, 205, 258, 259, 260, 264, 268, 274, 275, 277],
 'HENV-32': [154, 176, 199, 200, 205, 207, 268, 274, 275, 277, 534, 596],
 'HENV-117': [171, 204, 257, 555, 580, 582, 583, 586, 587, 588, 589],
 'm102.4': [172, 239, 270, 507, 542, 559, 577, 582, 586, 587, 589],
 'nAH1.3': [184, 185, 188, 189, 190, 447, 450, 468, 516, 517, 518]}

order_ab = ["m102.4", "HENV-26", "HENV-117", "HENV-103", "HENV-32", "nAH1.3"]


def generate_chart(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=1
    )
    chart = (
        alt.Chart(
            df,
            title=alt.Title(
                "Top Antibody Escape Mutations",
                subtitle="Hover over points to see escape at same site",
            ),
        )
        .mark_point(stroke="black")
        .encode(
            x=alt.X(
                "ab:O",
                sort=order_ab,
                title="Antibody",
                axis=alt.Axis(labelAngle=-90, grid=False),
            ),
            y=alt.Y(
                "effect:Q",
                title="Cell Entry of Top Escape",
                axis=alt.Axis(
                    grid=True, tickCount=4, values=[0.5, 0, -0.5, -1, -1.5, -2]
                ),
            ),
            size=alt.Size(
                "escape_median", legend=alt.Legend(title="Mean Escape By Mutation")
            ),
            xOffset="random:Q",
            tooltip=[
                "site",
                "wildtype",
                "mutant",
                "ab",
                "effect",
                "escape_median",
                "escape_std",
            ],
            color=alt.Color("ab").legend(None),
            opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.2)),
            strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
        )
        .transform_calculate(
            random="sqrt(-1*log(random()))*cos(2*PI*random())"
        )
        .properties(width=config["bubble_width"], height=config["bubble_height"])
        .add_params(variant_selector)
    )

    return chart


escape_bubble = generate_chart(filtered_df)
escape_bubble.display()
if mab_line_escape_plot is not None:
    escape_bubble.save(escape_bubble_plot)

# Load in wt nucleotide sequence (which is different than the 'wt' sequence from Library as it was codon optimized)
niv_m_wt = str(
    Bio.SeqIO.read(
        "data/custom_analyses_data/alignments/wild_type_seq.fasta", "fasta"
    ).seq
)

codon_table = {
    "ATA": "I",
    "ATC": "I",
    "ATT": "I",
    "ATG": "M",
    "ACA": "T",
    "ACC": "T",
    "ACG": "T",
    "ACT": "T",
    "AAC": "N",
    "AAT": "N",
    "AAA": "K",
    "AAG": "K",
    "AGC": "S",
    "AGT": "S",
    "AGA": "R",
    "AGG": "R",
    "CTA": "L",
    "CTC": "L",
    "CTG": "L",
    "CTT": "L",
    "CCA": "P",
    "CCC": "P",
    "CCG": "P",
    "CCT": "P",
    "CAC": "H",
    "CAT": "H",
    "CAA": "Q",
    "CAG": "Q",
    "CGA": "R",
    "CGC": "R",
    "CGG": "R",
    "CGT": "R",
    "GTA": "V",
    "GTC": "V",
    "GTG": "V",
    "GTT": "V",
    "GCA": "A",
    "GCC": "A",
    "GCG": "A",
    "GCT": "A",
    "GAC": "D",
    "GAT": "D",
    "GAA": "E",
    "GAG": "E",
    "GGA": "G",
    "GGC": "G",
    "GGG": "G",
    "GGT": "G",
    "TCA": "S",
    "TCC": "S",
    "TCG": "S",
    "TCT": "S",
    "TTC": "F",
    "TTT": "F",
    "TTA": "L",
    "TTG": "L",
    "TAC": "Y",
    "TAT": "Y",
    "TAA": "*",
    "TAG": "*",
    "TGC": "C",
    "TGT": "C",
    "TGA": "*",
    "TGG": "W",
}


def find_closest_codon(wt_codon, mutant_aa):
    mutant_codons = [codon for codon, aa in codon_table.items() if aa == mutant_aa]
    min_mutations = 3  # Maximum mutations possible
    closest_codon = None
    for m_codon in mutant_codons:
        mutations = sum([1 for c1, c2 in zip(wt_codon, m_codon) if c1 != c2])
        if mutations < min_mutations:
            min_mutations = mutations
            closest_codon = m_codon
    return closest_codon, min_mutations


# Function to extract codon for a given site
def extract_codon(site):
    idx = (site - 1) * 3
    return niv_m_wt[idx : idx + 3]


def extract_codon_niv_b(site):
    idx = (site - 1) * 3
    return niv_m_wt[idx : idx + 3]


def apply_codon_to_df(df, extract_func):
    df["wt_codon"] = df["site"].apply(extract_func)
    df["closest_mutant_codon"] = df.apply(
        lambda row: find_closest_codon(row["wt_codon"], row["mutant"])[0], axis=1
    )
    df["min_mutations"] = df.apply(
        lambda row: find_closest_codon(row["wt_codon"], row["mutant"])[1], axis=1
    )
    return df


combined_df = apply_codon_to_df(combined_df, extract_codon)
filtered_df = apply_codon_to_df(filtered_df, extract_codon)

def generate_chart_all(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=1
    )
    radio = alt.binding_radio(
        options=[1, 2, 3], labels=["1", "2", "3"], name="Min Mutations:"
    )
    mutation_selector = alt.param(name="MutationSelector", value=1, bind=radio)

    slider = alt.binding_range(min=0.2, max=1.6, step=0.1, name="median_escape")
    selector = alt.param(name="SelectorName", value=0.2, bind=slider)

    chart = (
        alt.Chart(
            df,
            title=alt.Title(
                "Antibody Escape Mutations",
                subtitle="Hover over points to see escape at same site",
            ),
        )
        .mark_point(filled=True, stroke="black")
        .encode(
            x=alt.X(
                "ab:O",
                sort=order_ab,
                title="Antibody",
                axis=alt.Axis(labelAngle=-90, grid=False),
            ),
            y=alt.Y(
                "effect:Q",
                title="Cell Entry of Top Escape",
                axis=alt.Axis(
                    grid=True, tickCount=4, values=[0.5, 0, -0.5, -1, -1.5, -2]
                ),
            ),
            size=alt.Size(
                "escape_median", legend=alt.Legend(title="Mean Escape By Mutation")
            ),
            xOffset="random:Q",
            tooltip=[
                "site",
                "wildtype",
                "mutant",
                "ab",
                "effect",
                "escape_median",
                "escape_std",
            ],
            color=alt.Color("ab").legend(None),
            opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.4)),
            strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
        )
        .transform_calculate(
            random="sqrt(-1*log(random()))*cos(2*PI*random())"
            # random='random'
        )
        #.properties(width=config["bubble_width"], height=config["bubble_height"])
        .properties(width=200,height=250)
        .add_params(variant_selector, mutation_selector, selector)
        .transform_filter(
            (alt.datum.min_mutations == mutation_selector)
            & (alt.datum.escape_median > selector)
        )
    )

    return chart


#all_escape = generate_chart_all(combined_df.query("escape_median >= 0.2"))
all_escape = generate_chart_all(filtered_df)

all_escape.display()

# Make combined figure
combined_bubble_plots = (escape_bubble | all_escape)
combined_bubble_plots.display()

def plot_escape_and_mutations_away(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=1
    )
    radio = alt.binding_radio(options=[1, 2, 3], name="Min Mutations:")
    mutation_selector = alt.param(name="MutationSelector", value=1, bind=radio)

    chart = (
        alt.Chart(
            df,
            title=alt.Title(
                "Top Antibody Escape Mutations",
                subtitle="By # of nucleotide mutations away",
            ),
        )
        .mark_point(filled=True, stroke="black",strokeWidth=0.75,opacity=0.3)
        .encode(
            x=alt.X(
                "ab:O",
                sort=order_ab,
                title='Antibody',
                axis=alt.Axis(labelAngle=-90, grid=False),
            ),
            y=alt.Y(
                "effect:Q",
                title="Cell Entry of Escape Mutants",
                axis=alt.Axis(
                    grid=True, tickCount=4, values=[0.5, 0, -0.5, -1, -1.5, -2]
                ),
            ),  # 'Q' denotes a quantitative variable
            size=alt.Size("escape_median", legend=alt.Legend(title="Escape of Mutant")),
            xOffset="random:Q",
            tooltip=["ab", "effect", "escape_median", "site", "mutant"],
            #opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.4)),
            #strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
            color=alt.Color("ab:N").legend(None),
        )
        .transform_calculate(
            # random='random()'
            random="sqrt(-2*log(random()))*cos(2*PI*random())"
        )
        .properties(width=200, height=config["bubble_height"])
        .add_params(variant_selector, mutation_selector)
        .transform_filter((alt.datum.min_mutations == mutation_selector))
    )
    return chart


bubble_plot_1_mut_away = plot_escape_and_mutations_away(filtered_df)
bubble_plot_1_mut_away.display()
if mab_line_escape_plot is not None:
    bubble_plot_1_mut_away.save(bubble_1_mut_plot)

def plot_escape_and_mutations_away_summed(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=1
    )
    aggregated_df = df.groupby(['site','ab']).agg({
        'escape_median': 'sum',
        'wildtype': 'first',
        #'ab': 'first',
        'effect': 'median',
    }).reset_index()
    aggregated_df = aggregated_df.query('escape_median > 2')
    #display(aggregated_df)
    
    chart = (
        alt.Chart(
            aggregated_df,
        )
        .mark_point(filled=True, stroke="black",strokeWidth=0.75,opacity=0.3)
        .encode(
            x=alt.X(
                "ab:O",
                sort=order_ab,
                title='Antibody',
                axis=alt.Axis(labelAngle=-90, grid=True),
            ),
            y=alt.Y(
                "effect:Q",
                title="Cell Entry of Escape Mutants",
                axis=alt.Axis(
                    grid=True, tickCount=4, #values=[0.5, 0, -0.5, -1, -1.5, -2]
                ),
            ),  
            size=alt.Size("escape_median", legend=alt.Legend(title="Escape Score")),
            xOffset="random:Q",
            tooltip=["ab", "effect", "escape_median", "site"],
            #opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.4)),
            #strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
            color=alt.Color("ab:N").legend(None),
        )
        .transform_calculate(
            # random='random()'
            random="sqrt(-2*log(random()))*cos(2*PI*random())"
        )
        .properties(width=150, height=config["bubble_height"])
        .add_params(variant_selector)
    )
    return chart


bubble_plot_1_mut_away = plot_escape_and_mutations_away_summed(combined_df)
bubble_plot_1_mut_away.display()
#if mab_line_escape_plot is not None:
#    bubble_plot_1_mut_away.save(bubble_1_mut_plot)

def find_overlapping_escape(df):
    slider = alt.binding_range(
        min=config["min_func_effect_for_ab"], max=0, step=0.25, name="effect"
    )
    selector = alt.param(name="SelectorName", value=-4, bind=slider)

    radio = alt.binding_radio(options=[1, 2, 3], name="Min Mutations:")
    mutation_selector = alt.param(name="MutationSelector", value=1, bind=radio)

    df_filtered = df
    # Group by 'site' and 'mutant', count the unique 'ab' values for each group
    grouped = df_filtered.groupby(["site", "mutant"])["ab"].nunique().reset_index()

    # Filter groups where the count of unique 'ab' values is at least 2
    result = grouped[grouped["ab"] >= 2]

    # Merge the result with the original dataframe to get the full rows
    df_result = pd.merge(df, result[["site", "mutant"]], on=["site", "mutant"])
    df_result["mutation_number"] = (
        df_result["mutation"].str.extract("(\d+)").astype(int)
    )
    base = (
        (
            alt.Chart(df_result, title=alt.Title("Shared antibody escape mutations"))
            .mark_rect()
            .encode(
                x=alt.X(
                    "mutation:O",
                    title="Site",
                    sort=alt.EncodingSortField(field="mutation_number"),
                    axis=alt.Axis(labelAngle=-90, grid=False),
                ),
                y=alt.Y(
                    "ab:O", title="Mutant", sort=order_ab, axis=alt.Axis(grid=False)
                ),  # Apply custom sort order here
                color="escape_median",
                tooltip=[
                    "site",
                    "wildtype",
                    "mutant",
                    "escape_median",
                    "min_mutations",
                ],
            )
        )
        .properties(height=200, width=400)
        .add_params(selector, mutation_selector)
        .transform_filter(
            (alt.datum.effect >= selector)
            & (alt.datum.min_mutations == mutation_selector)
        )
    )
    return base


overlap_escape = find_overlapping_escape(combined_df.query('escape_median > 0.4'))
overlap_escape.display()
if mab_line_escape_plot is not None:
    overlap_escape.save(overlap_escape_plot)

def plot_line_escape(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, fields=["site"], value=0
    )
    # Group by 'site' and 'mutant', count the unique 'ab' values for each group
    summed = df.groupby(["site", "ab"])["escape_median"].sum().reset_index()
    empty_chart = []
    ab_list = ["m102.4", "HENV-26", "HENV-117", "HENV-103", "HENV-32", "nAH1.3"]
    for idx, ab in enumerate(ab_list):
        tmp_df = summed[summed["ab"] == ab]
        # color = '#1f4e79'
        if ab in ["m102.4", "HENV-26", "HENV-117"]:
            color = "#1f4e79"
        if ab in ["HENV-103", "HENV-32"]:
            color = "#ff7f0e"
        if ab in ["nAH1.3"]:
            color = "#2ca02c"

        # Conditionally set the x-axis labels and title for the last plot
        is_last_plot = idx == len(ab_list) - 1
        x_axis = alt.Axis(
            values=[100, 200, 300, 400, 500, 600],
            tickCount=6,
            labelAngle=-90,
            grid=True,
            labelExpr="datum.value % 100 === 0 ? datum.value : ''",
            title="Site" if is_last_plot else None,
            labels=is_last_plot,
        )  # Only show labels for the last plot
        base = (
            alt.Chart(tmp_df)
            .mark_line(size=1, color=color)
            .encode(
                x=alt.X("site:O", axis=x_axis),
                y=alt.Y("escape_median", title=f"{ab}", axis=alt.Axis(grid=True)),
            )
            .properties(
                width=config["large_line_width"], height=config["large_line_height"]
            )
        )
        point = (
            base.mark_point(color="black", size=10, filled=True)
            .encode(
                x=alt.X("site:O", axis=x_axis),
                y=alt.Y(
                    "escape_median",
                    title=f"{ab}",
                    axis=alt.Axis(
                        grid=True,
                    ),
                ),
                size=alt.condition(variant_selector, alt.value(100), alt.value(15)),
                color=alt.condition(
                    variant_selector, alt.value("black"), alt.value(color)
                ),
                tooltip=["site", "escape_median"],
            )
            .add_params(variant_selector)
        )
        chart = base + point
        empty_chart.append(chart)

    # Use configure_concat to adjust spacing between vertically concatenated plots
    combined_chart = (
        alt.vconcat(*empty_chart, spacing=1)
        .resolve_scale(y="independent", x="shared", color="independent")
        .properties(
            title=alt.Title(
                "Summed Antibody Escape by Site", subtitle="Colored by epitope"
            )
        )
    )

    return combined_chart


tmp_line = plot_line_escape(combined_df)
tmp_line.display()
if mab_line_escape_plot is not None:
    tmp_line.save(mab_line_escape_plot)

def calculate_min_distances(pdb_path, source_chain_id, target_chain_ids, name):
    # Initialize the PDB parser and load the structure
    parser = PDB.PDBParser(QUIET=True)
    structure = parser.get_structure("structure_id", pdb_path)

    source_chain = structure[0][source_chain_id]
    target_chains = [structure[0][chain_id] for chain_id in target_chain_ids]

    data = []

    for residueA in source_chain:
        if residueA.resname in ["HOH", "WAT", "IPA", "NAG"]:
            continue

        min_distance = float("inf")
        closest_residueB = None
        closest_chain_id = None
        residues_within_4 = 0

        for target_chain in target_chains:
            for residueB in target_chain:
                if residueB.resname in ["HOH", "WAT", "IPA"]:
                    continue

                # Check for residues within 4 angstroms
                is_within_4 = False
                for atomA in residueA:
                    for atomB in residueB:
                        distance = atomA - atomB
                        if distance < min_distance:
                            min_distance = distance
                            closest_residueB = residueB
                            closest_chain_id = target_chain.get_id()
                        if distance < 4:
                            is_within_4 = True
                if is_within_4:
                    residues_within_4 += 1

        data.append(
            {
                "wildtype": residueA.resname,
                "site": residueA.id[1],
                "chain": closest_chain_id,
                "residue": closest_residueB.id[1],
                "residue_name": closest_residueB.resname,
                "distance": min_distance,
                "residues_within_4": residues_within_4,
                "ab": name,
            }
        )

    # Convert data to pandas DataFrame
    df = pd.DataFrame(data)
    return df


def check_file(input_path, source_chain, target_chain, name, output_path):

    file_path = output_path

    if not os.path.exists(file_path):
        print(f"File {name} does not exist, running calculation")
        output_df = calculate_min_distances(
            input_path, source_chain, target_chain, name
        )
        print(f"done calculating for {file_path}")
        output_df.to_csv(output_path, index=False)
        return output_df
    else:
        print("File already exists,loading from disk")
        output_df = pd.read_csv(output_path)
        return output_df


pdb_path_26 = "data/custom_analyses_data/crystal_structures/6vy5.pdb"
source_chain_26 = "A"
target_chains_26 = ["H", "L"]
output_path_26 = "results/distances/df_HENV26_atomic_distances.csv"

pdb_path_32 = "data/custom_analyses_data/crystal_structures/6vy4.pdb"
source_chain_32 = "A"
target_chains_32 = ["H", "L"]
output_path_32 = "results/distances/df_HENV32_atomic_distances.csv"

pdb_path_nah = "data/custom_analyses_data/crystal_structures/7txz.pdb"
source_chain_nah = "A"
target_chains_nah = ["F", "E"]
output_path_nah = "results/distances/df_nAH_atomic_distances.csv"

pdb_path_m102 = "data/custom_analyses_data/crystal_structures/6cmg.pdb"
source_chain_m102 = "A"
target_chains_m102 = ["B", "C"]
output_path_m102 = "results/distances/df_m102_atomic_distances.csv"


df_HENV26 = check_file(
    pdb_path_26, source_chain_26, target_chains_26, "HENV-26", output_path_26
)
df_HENV32 = check_file(
    pdb_path_32, source_chain_32, target_chains_32, "HENV-32", output_path_32
)
df_nah = check_file(
    pdb_path_nah, source_chain_nah, target_chains_nah, "nAH1.3", output_path_nah
)
df_nah["chain"].replace(
    {"E": "H", "F": "L"}, inplace=True
)  # Fix naming so consistent heavy and light chain naming
df_m102 = check_file(
    pdb_path_m102, source_chain_m102, target_chains_m102, "m102.4", output_path_m102
)
df_m102["chain"].replace(
    {"C": "H", "B": "L"}, inplace=True
)  # Fix naming so consistent heavy and light chain naming

File already exists,loading from disk
File already exists,loading from disk
File already exists,loading from disk
File already exists,loading from disk

def find_close_mab_sites(df, name):
    unique_sites = df.query("distance <= 4")["site"].unique()
    mab_site_list = list(unique_sites)
    print(f"Close sites for mAb {name} are: {mab_site_list}")
    return mab_site_list


### First find RBP sites that are close to mAb residues
nah_close = find_close_mab_sites(df_nah, "nAH1.3")
HENV26_close = find_close_mab_sites(df_HENV26, "HENV-26")
HENV32_close = find_close_mab_sites(df_HENV32, "HENV-32")
m102_close = find_close_mab_sites(df_m102, "m102.4")

### Now combined the close residues AND the top escape sites identified previously
nah_combined_sites = sites_dict["nAH1.3"] + nah_close
HENV26_combined_sites = sites_dict["HENV-26"] + HENV26_close
HENV32_combined_sites = sites_dict["HENV-32"] + HENV32_close
m102_combined_sites = sites_dict["m102.4"] + m102_close

Close sites for mAb nAH1.3 are: [172, 183, 184, 185, 186, 187, 188, 190, 191, 358, 449, 450, 451, 472, 515, 516, 517, 518, 570]
Close sites for mAb HENV-26 are: [389, 401, 403, 404, 458, 488, 489, 490, 491, 492, 494, 497, 501, 504, 505, 506, 528, 529, 530, 531, 532, 533, 555, 556, 557, 581, 586]
Close sites for mAb HENV-32 are: [196, 199, 200, 201, 202, 203, 205, 206, 207, 210, 254, 256, 258, 260, 262, 263, 264, 266, 553]
Close sites for mAb m102.4 are: [239, 240, 241, 242, 305, 458, 488, 489, 490, 504, 505, 506, 507, 530, 532, 533, 555, 557, 559, 579, 580, 581, 588]

def make_distance(df):
    subset_df = df[["site", "distance"]].copy()
    subset_df["mutant"] = "distance"
    subset_df["wildtype"] = ""
    subset_df["effect"] = "escape_median"
    subset_df.rename(columns={"distance": "value"}, inplace=True)
    return subset_df


distance_nah_df = make_distance(df_nah)
distance_26_df = make_distance(df_HENV26)
distance_32_df = make_distance(df_HENV32)
distance_m102_df = make_distance(df_m102)

display(distance_m102_df)

def make_empty_df_with_distance(ab, distance_file):
    # print(ab)
    sites = range(71, 603)
    amino_acids = [
        "A",
        "C",
        "D",
        "E",
        "F",
        "G",
        "H",
        "I",
        "K",
        "L",
        "M",
        "N",
        "P",
        "Q",
        "R",
        "S",
        "T",
        "V",
        "W",
        "Y",
    ]
    # Create the combination of each site with each amino acid
    data = [{"site": site, "mutant": aa} for site in sites for aa in amino_acids]
    # Create the DataFrame
    empty_df = pd.DataFrame(data)
    all_sites_df = pd.merge(
        empty_df, combined_df.query(f'ab == "{ab}"'), on=["site", "mutant"], how="left"
    )
    df_melted = all_sites_df.melt(
        id_vars=["site", "mutant", "wildtype"],
        value_vars=["escape_median"],
        var_name="effect",
        value_name="value",
    )

    df_filtered = func_scores_E3_low_effect.melt(
        id_vars=["site", "mutant", "wildtype"],
        value_vars=["effect"],
        var_name="effect",
        value_name="value",
    )

    df_test = pd.concat([df_melted, df_filtered, distance_file], ignore_index=True)
    df_test["ab"] = ab
    return df_test


empty_df_m102 = make_empty_df_with_distance("m102.4", distance_m102_df)
empty_df_HENV26 = make_empty_df_with_distance("HENV-26", distance_26_df)
empty_df_HENV32 = make_empty_df_with_distance("HENV-32", distance_32_df)
empty_df_nah = make_empty_df_with_distance("nAH1.3", distance_nah_df)


def make_empty_df(ab):
    sites = range(71, 603)
    amino_acids = [
        "A",
        "C",
        "D",
        "E",
        "F",
        "G",
        "H",
        "I",
        "K",
        "L",
        "M",
        "N",
        "P",
        "Q",
        "R",
        "S",
        "T",
        "V",
        "W",
        "Y",
    ]
    # Create the combination of each site with each amino acid
    data = [{"site": site, "mutant": aa} for site in sites for aa in amino_acids]
    # Create the DataFrame
    empty_df = pd.DataFrame(data)
    all_sites_df = pd.merge(
        empty_df, combined_df.query(f'ab == "{ab}"'), on=["site", "mutant"], how="left"
    )
    df_melted = all_sites_df.melt(
        id_vars=["site", "mutant", "wildtype"],
        value_vars=["escape_median"],
        var_name="effect",
        value_name="value",
    )

    df_filtered = func_scores_E3_low_effect.melt(
        id_vars=["site", "mutant", "wildtype"],
        value_vars=["effect"],
        var_name="effect",
        value_name="value",
    )

    df_test = pd.concat([df_melted, df_filtered], ignore_index=True)
    df_test["ab"] = ab
    return df_test


empty_df_HENV117 = make_empty_df("HENV-117")
empty_df_HENV103 = make_empty_df("HENV-103")

combined_ab = pd.concat(
    [
        empty_df_m102,
        empty_df_HENV26,
        empty_df_HENV32,
        empty_df_nah,
        empty_df_HENV117,
        empty_df_HENV103,
    ]
)
display(combined_ab)

def plot_distance_only(df, trigger):
    custom_order = [
        "distance",
        "R",
        "K",
        "H",
        "D",
        "E",
        "Q",
        "N",
        "S",
        "T",
        "Y",
        "W",
        "F",
        "A",
        "I",
        "L",
        "M",
        "V",
        "G",
        "P",
        "C",
    ]
    all_residues = range(71, 603)
    final_df = df
    final_df = final_df.sort_values(
        "site"
    )  # Sort the dataframe by 'site' to ensure that duplicates are detected correctly.
    sort_order = {
        mutant: i for i, mutant in enumerate(custom_order)
    }  # Create a dictionary that maps each mutant to its sort rank based on the custom order
    final_df["mutant_rank"] = final_df["mutant"].map(
        sort_order
    )  # Map the 'mutant' column to these ranks

    final_df = final_df.sort_values(
        "mutant_rank"
    )  # Now sort the dataframe by this rank
    final_df = final_df.drop(
        columns=["mutant_rank"]
    )  # Drop the 'mutant_rank' column as it is no longer needed after sorting
    sites = sorted(final_df["site"].unique(), key=lambda x: float(x))
    ab_list = ["m102.4", "HENV-26", "HENV-117", "HENV-103", "HENV-32", "nAH1.3"]
    empty_chart = []  # setup collection for charts
    for idx, ab in enumerate(ab_list):
        tmp_df = final_df[final_df["ab"] == ab]
        if ab == "m102.4":
            site_subset = m102_combined_sites
            # legend_conditional = alt.Legend(title='Distance to mAb')
        if ab == "HENV-26":
            site_subset = HENV26_combined_sites
            # legend_conditional = alt.Legend(title='Distance to mAb')
        if ab == "HENV-32":
            site_subset = HENV32_combined_sites
            # legend_conditional = alt.Legend(title='Distance to mAb')
        if ab == "HENV-103":
            site_subset = sites_dict["HENV-103"]
            # legend_conditional = alt.Legend(title=None)
        if ab == "HENV-117":
            site_subset = sites_dict["HENV-117"]
            # legend_conditional = alt.Legend(title=None)
        if ab == "nAH1.3":
            site_subset = nah_combined_sites
            # legend_conditional = alt.Legend(title='Distance to mAb')

        # select which sites you will show
        if trigger == True:
            tmp_df = tmp_df[tmp_df["site"].isin(site_subset)]
            x_axis = alt.Axis(
                labelAngle=-90,
                # labelExpr="datum.value % 10 === 0 ? datum.value : ''",
                title="Site",
            )
        else:
            tmp_df = tmp_df[tmp_df["site"].isin(all_residues)]

            # Conditionally set the x-axis labels and title for the last plot
            is_last_plot = idx == len(ab_list) - 1
            x_axis = alt.Axis(
                labelAngle=-90,
                labelExpr="datum.value % 10 === 0 ? datum.value : ''",
                title="Site" if is_last_plot else None,
                labels=True,
            )  # Only show labels for the last plot

        # Prepare the color scales separately for distance and effects
        # Filter out 'distance' values before creating the effect heatmap
        effect_df = tmp_df[
            (tmp_df["mutant"] != "distance") & (tmp_df["effect"] != "effect")
        ]
        max_color = effect_df["value"].max()
        min_color = effect_df["value"].min()

        # Adjust color scheme for abs with little sensitizing mutations
        if min_color > -1:
            min_color = min_color - 1

        # Prepare the color scale for effects, Altair will automatically determine the domain
        color_scale_escape = alt.Scale(
            scheme="redblue", domainMid=0, domain=[min_color, max_color]
        )
        color_scale_entropy = alt.Scale(scheme="greens", domain=[0, 15], reverse=True)

        strokewidth_size = 0.25

        unique_wildtypes_df = tmp_df.drop_duplicates(subset=["site", "wildtype"])

        # The chart for the heatmap
        base = (
            alt.Chart(tmp_df, title=f"{ab}")
            .encode(
                x=alt.X("site:O", title="Site", sort=sites, axis=x_axis),
                y=alt.Y(
                    "mutant",
                    title="Amino Acid",
                    sort=alt.EncodingSortField(field="sort_order", order="ascending"),
                    axis=alt.Axis(grid=False),
                ),  # Apply custom sort order here
                tooltip=["site", "wildtype", "mutant", "value"],
            )
            .properties(width=alt.Step(10), height=alt.Step(11))
        )
        # Heatmap for distance
        chart_empty = (
            base.mark_rect(color="#e6e7e8")
            .encode()
            .transform_filter(alt.datum.effect == "escape_median")
        )
        # Heatmap for effect
        chart_effect = (
            base.mark_rect(stroke="black", strokeWidth=strokewidth_size)
            .encode(
                color=alt.condition(
                    'datum.mutant != "distance"',
                    alt.Color(
                        "value:Q",
                        scale=color_scale_escape,
                        legend=alt.Legend(title=f"{ab} Escape"),
                    ),
                    alt.value("transparent"),
                ),
            )
            .transform_filter(alt.datum.effect == "escape_median")
        )

        # Heatmap for distance
        if ab in ["m102.4", "HENV-26", "HENV-32", "nAH1.3"]:
            chart_distance = (
                base.mark_rect()
                .encode(
                    color=alt.condition(
                        'datum.mutant == "distance"',
                        alt.Color(
                            "value:Q",
                            scale=color_scale_entropy,
                            legend=alt.Legend(title="Distance to mAb"),
                        ),
                        alt.value("transparent"),
                    )
                )
                .transform_filter(alt.datum.effect == "escape_median")
            )
        else:
            chart_distance = (
                base.mark_rect(color="transparent")
                .encode(
                    # color=alt.Color('white'),
                    # alt.Color('value:Q', scale=color_scale_entropy,legend=alt.Legend(title='Distance to mAb')),
                    # alt.value('transparent'))
                )
                .transform_filter(alt.datum.effect == "escape_median")
            )
        # Heatmap for distance
        chart_filtered = (
            base.mark_rect(
                color="#939598", stroke="black", strokeWidth=strokewidth_size
            )
            .encode()
            .transform_filter(alt.datum.effect == "effect")
        )

        # The layer for the wildtype boxes
        wildtype_layer_box = (
            alt.Chart(unique_wildtypes_df)
            .mark_rect(color="white", stroke="black", strokeWidth=strokewidth_size)
            .encode(
                x=alt.X("site:O", sort=sites),
                y=alt.Y(
                    "wildtype",
                    sort=alt.EncodingSortField(field="sort_order", order="ascending"),
                ),
                opacity=alt.value(1),
            )
            .transform_filter(
                (alt.datum.wildtype != "")
                & (alt.datum.wildtype != None)
                & (alt.datum.value != None)
            )
        )
        # The layer for the wildtype amino acids
        wildtype_layer = (
            alt.Chart(unique_wildtypes_df)
            .mark_text(color="black", text="X", size=8)
            .encode(
                x=alt.X("site:O", sort=sites),
                y=alt.Y(
                    "wildtype",
                    sort=alt.EncodingSortField(field="sort_order", order="ascending"),
                ),
                opacity=alt.value(1),
            )
            .transform_filter(
                (alt.datum.wildtype != "")
                & (alt.datum.wildtype != None)
                & (alt.datum.value != None)
            )
        )

        # Combine the heatmap layer with the wildtype layer
        chart = alt.layer(
            chart_empty,
            chart_effect,
            chart_distance,
            chart_filtered,
            wildtype_layer_box,
            wildtype_layer,
        ).resolve_scale(color="independent")
        empty_chart.append(chart)
    combined_chart = (
        alt.vconcat(*empty_chart, spacing=1)
        .resolve_scale(y="shared", x="independent", color="independent")
        .configure_title(
            anchor="start",  # Aligns the title to the left ('middle' for center, 'end' for right)
            offset=10,  # Adjusts the distance of the title from the chart
            orient="top",  # Positions the title at the top; use 'bottom' to position at the bottom
        )
    )
    return combined_chart


mab_plot = plot_distance_only(combined_ab, True)
mab_plot.display()
if mab_line_escape_plot is not None:
    mab_plot.save(mab_plot_top)

mab_all = plot_distance_only(combined_ab, False)
mab_all.display()
if mab_line_escape_plot is not None:
    mab_all.save(mab_plot_all)

bind_df = pd.read_csv(binding_data)
binding_df = bind_df.groupby("site")["binding_median"].median().reset_index()


def make_empty_binding():
    sites = range(71, 603)
    data = [{"site": site} for site in sites]
    empty_df = pd.DataFrame(data)
    empty_df = pd.merge(empty_df, binding_df, on="site", how="left")
    empty_df = empty_df.rename(columns={"binding_median": "value"})
    empty_df["effect"] = "escape_median"
    empty_df["ab"] = "Ephrin-B2 binding"
    return empty_df


binding_empty = make_empty_binding()

escape_df = combined_df.groupby(["ab", "site"])["escape_median"].median().reset_index()


def make_empty_df(ab):
    sites = range(71, 603)
    data = [{"site": site} for site in sites]

    # Create the DataFrame
    empty_df = pd.DataFrame(data)

    all_sites_df = pd.merge(
        empty_df, escape_df.query(f'ab == "{ab}"'), on=["site"], how="left"
    )

    df_melted = all_sites_df.melt(
        id_vars=["site"],
        value_vars=["escape_median"],
        var_name="effect",
        value_name="value",
    )

    df_test = pd.concat([df_melted], ignore_index=True)
    df_test["ab"] = ab
    return df_test


ab_list = ["m102.4", "HENV-26", "HENV-117", "HENV-103", "HENV-32", "nAH1.3"]
# ab_list = ['HENV-32']

empty = []
for ab in ab_list:
    tmp_df = make_empty_df(ab)
    empty.append(tmp_df)
all_empties_df = pd.concat(empty, ignore_index=True)
all_empties_df = pd.concat([all_empties_df, binding_empty])
display(all_empties_df)

def make_heatmap_with_binding(df):
    # Define the custom sort order directly in the encoding
    sort_order = [
        "NiV Polymorphism",
        "Ephrin-B2 binding",
        "m102.4",
        "HENV-26",
        "HENV-117",
        "HENV-103",
        "HENV-32",
        "nAH1.3",
    ]
    full_ranges = [
        list(range(start, end))
        for start, end in [(71, 181), (181, 291), (291, 401), (401, 511), (511, 603)]
    ]

    # container to hold the charts
    charts = []
    color_scale_effect = alt.Scale(scheme="redblue", domainMid=0)
    color_scale_binding = alt.Scale(scheme="redblue", domainMid=0)

    for idx, subset in enumerate(full_ranges):
        subset_df = df[df["site"].isin(subset)]  # for the wrapping of sites
        is_last_plot = idx == len(full_ranges) - 1
        x_axis = alt.Axis(
            labelAngle=-90,
            labelExpr="datum.value % 10 === 0 ? datum.value : ''",
            title="Site" if is_last_plot else None,
            labels=True,
        )  # Only show labels for the last plot

        effect_legend = (
            alt.Legend(title="Antibody Escape") if is_last_plot else None
        )  # ,direction='horizontal',gradientLength=50,titleAnchor='middle',tickCount=3,labelAlign='center')
        binding_legend = (
            alt.Legend(title="Henipavirus Entropy") if is_last_plot else None
        )  # ,direction='horizontal',gradientLength=50,titleAnchor='middle',labelAlign='center')
        print(is_last_plot)
        print(effect_legend)
        base = (
            alt.Chart(subset_df)
            .encode(
                x=alt.X("site:O", title="Site", axis=x_axis),
                y=alt.Y(
                    "ab", title=None, sort=sort_order, axis=alt.Axis(grid=False)
                ),  # Correctly apply custom sort order
                tooltip=["site", "value"],
            )
            .properties(width=alt.Step(10), height=alt.Step(11))
        )

        # Define the chart for empty cells
        chart_empty = base.mark_rect(color="#e6e7e8").transform_filter(
            alt.datum.effect == "escape_median"
        )

        # Define the chart for cells with effect
        chart_effect = (
            base.mark_rect(stroke="black", strokeWidth=0.25)
            .encode(
                color=alt.condition(
                    'datum.effect == "escape_median"',
                    alt.Color(
                        "value:Q", scale=color_scale_effect, legend=effect_legend
                    ),  # Define a color scale
                    alt.value("transparent"),
                )
            )
            .transform_filter(alt.datum.effect == "escape_median")
        )

        chart_binding = (
            base.mark_rect(strokeWidth=1.1)
            .encode(
                stroke=alt.value("value"),
                color=alt.condition(
                    'datum.effect == "escape_median"',
                    alt.Color(
                        "value:Q", scale=color_scale_binding, legend=binding_legend
                    ),
                    alt.value("transparent"),
                ),
            )
            .transform_filter(alt.datum.ab == "Ephrin-B2 binding")
        )

        chart_poly = (
            base.mark_rect(color="black")
            .encode()
            .transform_filter(alt.datum.ab == "NiV Polymorphism")
        )
        # Layer the charts using `layer` instead of `+`
        chart = alt.layer(
            chart_empty, chart_effect, chart_binding, chart_poly
        )  # .resolve_scale(color='shared')
        charts.append(chart)
    combined_chart = alt.vconcat(
        *charts, spacing=5, title="Heatmap of median mAb escape and Ephrin-B2 binding"
    )  

    return combined_chart


# Assuming `all_empties_df` is your DataFrame and already defined
chart = make_heatmap_with_binding(all_empties_df)
chart.display()
if mab_line_escape_plot is not None:
    chart.save(aggregate_mab_and_binding)

False
None
False
None
False
None
False
None
True
Legend({
  title: 'Antibody Escape'
})

def make_contact():
    df = pd.DataFrame({"site": niv_poly, "contact": [0.0] * len(niv_poly)})
    df = df[["site", "contact"]]
    # df['mutant'] = 'contact'
    df["ab"] = "NiV Polymorphism"
    df["effect"] = "median_escape"
    df.rename(columns={"contact": "value"}, inplace=True)
    return df


niv_poly = [
    82,
    89,
    135,
    172,
    228,
    236,
    274,
    288,
    299,
    325,
    328,
    329,
    335,
    339,
    344,
    376,
    384,
    385,
    386,
    421,
    423,
    424,
    426,
    427,
    470,
    478,
    481,
    498,
    502,
    545,
]
contact_df = make_contact()

bind_df = pd.read_csv("results/filtered_data/E2_binding_filtered.csv")
binding_df = bind_df.groupby("site")["binding_median"].max().reset_index()


def make_empty_binding():
    sites = range(71, 603)
    data = [{"site": site} for site in sites]
    empty_df = pd.DataFrame(data)
    empty_df = pd.merge(empty_df, binding_df, on="site", how="left")
    empty_df = empty_df.rename(columns={"binding_median": "value"})
    empty_df["effect"] = "escape_median"
    empty_df["ab"] = "Ephrin-B2 binding"
    return empty_df


binding_empty = make_empty_binding()

escape_df = combined_df.groupby(["ab", "site"])["escape_median"].max().reset_index()


def make_empty_df(ab):
    sites = range(71, 603)
    data = [{"site": site} for site in sites]

    # Create the DataFrame
    empty_df = pd.DataFrame(data)

    all_sites_df = pd.merge(
        empty_df, escape_df.query(f'ab == "{ab}"'), on=["site"], how="left"
    )

    df_melted = all_sites_df.melt(
        id_vars=["site"],
        value_vars=["escape_median"],
        var_name="effect",
        value_name="value",
    )

    df_test = pd.concat([df_melted], ignore_index=True)
    df_test["ab"] = ab
    return df_test


ab_list = ["m102.4", "HENV-26", "HENV-117", "HENV-103", "HENV-32", "nAH1.3"]

empty = []
for ab in ab_list:
    tmp_df = make_empty_df(ab)
    empty.append(tmp_df)
all_empties_df = pd.concat(empty, ignore_index=True)
all_empties_df = pd.concat([all_empties_df, contact_df])
display(all_empties_df)

def make_heatmap_with_polymorphisms(df):
    # Define the custom sort order directly in the encoding
    sort_order = [
        "NiV Polymorphism",
        "m102.4",
        "HENV-26",
        "HENV-117",
        "HENV-103",
        "HENV-32",
        "nAH1.3",
    ]
    # full_ranges = [list(range(start, end)) for start, end in [(71, 204), (204, 337), (337, 470), (470, 603)]]
    full_ranges = [
        list(range(start, end))
        for start, end in [(71, 181), (181, 291), (291, 401), (401, 511), (511, 603)]
    ]

    # container to hold the charts
    charts = []
    color_scale_effect = alt.Scale(scheme="redblue", domainMid=0, domain=[0, 2])
    color_scale_binding = alt.Scale(scheme="redblue", domainMid=0, domain=[-5, 2])

    # Flags for showing the legend only the first time
    effect_legend_added = True
    binding_legend_added = True
    for idx, subset in enumerate(full_ranges):
        subset_df = df[df["site"].isin(subset)]  # for the wrapping of sites
        is_last_plot = idx == len(full_ranges) - 1
        x_axis = alt.Axis(
            labelAngle=-90,
            labelExpr="datum.value % 10 === 0 ? datum.value : ''",
            title="Site" if is_last_plot else None,
            labels=True,
        )  # Only show labels for the last plot

        base = (
            alt.Chart(subset_df)
            .encode(
                x=alt.X("site:O", title="Site", axis=x_axis),
                y=alt.Y(
                    "ab", title=None, sort=sort_order, axis=alt.Axis(grid=False)
                ),  # Correctly apply custom sort order
                tooltip=["site", alt.Tooltip("value", format=".2f")],
            )
            .properties(width=alt.Step(10), height=alt.Step(11))
        )

        # Define the chart for empty cells
        chart_empty = base.mark_rect(color="#e6e7e8").transform_filter(
            alt.datum.effect == "escape_median"
        )
        if not effect_legend_added:
            # Define the chart for cells with effect
            chart_effect = (
                base.mark_rect(stroke="black", strokeWidth=0.25)
                .encode(
                    color=alt.condition(
                        'datum.effect == "escape_median"',
                        alt.Color(
                            "value:Q", scale=color_scale_effect
                        ),  # Define a color scale
                        alt.value("transparent"),
                    )
                )
                .transform_filter(alt.datum.effect == "escape_median")
            )
            effect_legend_added = True
        else:
            # Define the chart for cells with effect
            chart_effect = (
                base.mark_rect(stroke="black", strokeWidth=0.25)
                .encode(
                    color=alt.condition(
                        'datum.effect == "escape_median"',
                        alt.Color(
                            "value:Q", scale=color_scale_effect, legend=None
                        ),  # Define a color scale
                        alt.value("transparent"),
                    )
                )
                .transform_filter(alt.datum.effect == "escape_median")
            )
        if not binding_legend_added:
            chart_binding = (
                base.mark_rect(strokeWidth=1.1)
                .encode(
                    stroke=alt.value("value"),
                    color=alt.condition(
                        'datum.effect == "escape_median"',
                        alt.Color("value:Q", scale=color_scale_binding),
                        alt.value("transparent"),
                    ),
                )
                .transform_filter(alt.datum.ab == "Ephrin-B2 binding")
            )
            binding_legend_added = True
        else:
            chart_binding = (
                base.mark_rect(strokeWidth=1.1)
                .encode(
                    stroke=alt.value("value"),
                    color=alt.condition(
                        'datum.effect == "escape_median"',
                        alt.Color("value:Q", scale=color_scale_binding, legend=None),
                        alt.value("transparent"),
                    ),
                )
                .transform_filter(alt.datum.ab == "Ephrin-B2 binding")
            )

        chart_poly = (
            base.mark_rect(color="black")
            .encode()
            .transform_filter(alt.datum.ab == "NiV Polymorphism")
        )
        # Layer the charts using `layer` instead of `+`
        chart = alt.layer(chart_empty, chart_effect, chart_poly).resolve_scale(
            color="independent"
        )
        charts.append(chart)
    combined_chart = alt.vconcat(
        *charts, spacing=5, title="Heatmap of max mAb escape and Nipah Polymorphisms"
    ).resolve_scale(y="shared", x="independent", color="shared")

    return combined_chart


# Assuming `all_empties_df` is your DataFrame and already defined
chart = make_heatmap_with_polymorphisms(all_empties_df)
chart.display()
if mab_line_escape_plot is not None:
    chart.save(aggregate_mab_and_niv_polymorphism)

display(combined_df)

def make_polymorphism_escape(df):
    df['is_poly'] = df['site'].isin(niv_poly)
    aggregated_df = df.groupby(['site', 'ab']).agg({
        'escape_median': 'sum',
        'wildtype': 'first',
        'is_poly': 'first'
    }).reset_index()
    empty_chart = []
    antibodies = ['m102.4', 'HENV-26', 'HENV-117', 'HENV-103', 'HENV-32', 'nAH1.3']
    for index, ab in enumerate(antibodies):
        tmp_df = aggregated_df[aggregated_df['ab'] == ab]
        # Conditionally set the y-axis title for only the first chart
        y_axis_title = 'Summed Escape' if index == 0 else None
        
        base = alt.Chart(tmp_df).mark_point(size=25, opacity=0.2, filled=True,strokeWidth=0.5,stroke='black').encode(
            x=alt.X("is_poly", title=None, axis=alt.Axis(labelAngle=-90, grid=False)),
            xOffset="random:Q",
            y=alt.Y("escape_median", title=y_axis_title, axis=alt.Axis(grid=True, tickCount=2)),  
            tooltip=["site"],
            color=alt.Color('is_poly',title='Polymorphic Site'),
        ).transform_calculate(
            random="sqrt(-2*log(random()))*cos(2*PI*random())"
        ).properties(
            title={
                "text": f'{ab}',
                "fontSize": 10,  # Adjust font size as needed
                "align": "center",
                'anchor': "middle"
            },
            width=50,
        )
        empty_chart.append(base)
    combined_chart = alt.hconcat(*empty_chart, spacing=10).resolve_scale(y="independent", color="shared")

    return combined_chart





chart = make_polymorphism_escape(combined_df)
chart.display()

def make_polymorphism_escape(df):
    df['is_poly'] = df['site'].isin(niv_poly)
    aggregated_df = df.groupby(['site']).agg({
        'escape_median': 'median',
        'wildtype': 'first',
        'is_poly': 'first'
    }).reset_index()
    empty_chart = []
    #antibodies = ['m102.4', 'HENV-26', 'HENV-117', 'HENV-103', 'HENV-32', 'nAH1.3']
    #for index, ab in enumerate(antibodies):
        #tmp_df = aggregated_df[aggregated_df['ab'] == ab]
        # Conditionally set the y-axis title for only the first chart
        #y_axis_title = 'Summed Escape' if index == 0 else None
        
    base = alt.Chart(aggregated_df).mark_point(size=25, opacity=0.2, filled=True,strokeWidth=0.5,stroke='black').encode(
        x=alt.X("is_poly", title=None, axis=alt.Axis(labelAngle=-90, grid=False)),
        xOffset="random:Q",
        y=alt.Y("escape_median", title=None, axis=alt.Axis(grid=True, tickCount=5)),  
        tooltip=["site"],
        color=alt.Color('is_poly',title='Polymorphic Site'),
    ).transform_calculate(
        random="sqrt(-2*log(random()))*cos(2*PI*random())"
    ).properties(
        width=50,
    )
#        empty_chart.append(base)
#    combined_chart = alt.hconcat(*empty_chart, spacing=10).resolve_scale(y="independent", color="shared")

    return base





chart = make_polymorphism_escape(combined_df)
chart.display()

new_merged_df = pd.merge(
    combined_df,
    bind_df[["site", "wildtype", "mutant", "binding_median"]],
    on=["site", "wildtype", "mutant"],
    how="left",
)
new_merged_df = new_merged_df.drop(
    columns=[
        "mutation",
        "escape_std",
        "times_seen_ab",
        "show_site",
        "wt_codon",
        "closest_mutant_codon",
        "min_mutations",
    ]
)
new_merged_df = new_merged_df.round(2)

ab_list1 = ["m102.4", "HENV-26", "HENV-117"]
ab_list2 = ["HENV-103", "HENV-32"]
ab_list3 = ["nAH1.3"]


def plot_escape_vs_binding(df):
    variant_selector = alt.selection_point(
        on="mouseover", empty=False, nearest=True, fields=["site"], value=1
    )
    empty_chart1 = []
    for ab in ab_list1:
        tmp_df = df[df["ab"] == ab]
        base = (
            alt.Chart(tmp_df, title=alt.Title(f"{ab}", anchor="middle"))
            .mark_point(
                filled=True, size=15, color="#1f4e79", opacity=0.15, stroke="black"
            )
            .encode(
                alt.X(
                    "binding_median",
                    title="EFNB2 Binding",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                alt.Y(
                    "escape_median",
                    title="Antibody Escape",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                tooltip=[
                    "site",
                    "wildtype",
                    "mutant",
                    "escape_median",
                    "binding_median",
                ],
                opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.2)),
                size=alt.condition(variant_selector, alt.value(50), alt.value(20)),
                strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
            )
        )
        empty_chart1.append(base)
    combined_chart1 = alt.hconcat(*empty_chart1, spacing=5).resolve_scale(
        x="shared", y="shared"
    )
    empty_chart2 = []
    for ab in ab_list2:
        tmp_df = df[df["ab"] == ab]
        base = (
            alt.Chart(tmp_df, title=alt.Title(f"{ab}", anchor="middle"))
            .mark_point(
                filled=True, size=15, color="#ff7f0e", opacity=0.15, stroke="black"
            )
            .encode(
                alt.X(
                    "binding_median",
                    title="EFNB2 Binding",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                alt.Y(
                    "escape_median",
                    title="Antibody Escape",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                tooltip=[
                    "site",
                    "wildtype",
                    "mutant",
                    "escape_median",
                    "binding_median",
                ],
                opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.2)),
                size=alt.condition(variant_selector, alt.value(50), alt.value(20)),
                strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
            )
        )
        empty_chart2.append(base)
    combined_chart2 = alt.hconcat(*empty_chart2, spacing=5).resolve_scale(
        x="shared", y="shared"
    )

    empty_chart3 = []
    for ab in ab_list3:
        tmp_df = df[df["ab"] == ab]
        base3 = (
            alt.Chart(tmp_df, title=alt.Title(f"{ab}", anchor="middle"))
            .mark_point(
                filled=True, size=15, color="#2ca02c", opacity=0.15, stroke="black"
            )
            .encode(
                alt.X(
                    "binding_median",
                    title="EFNB2 Binding",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                alt.Y(
                    "escape_median",
                    title="Antibody Escape",
                    axis=alt.Axis(grid=True, tickCount=3),
                ),
                tooltip=[
                    "site",
                    "wildtype",
                    "mutant",
                    "escape_median",
                    "binding_median",
                ],
                opacity=alt.condition(variant_selector, alt.value(1), alt.value(0.2)),
                size=alt.condition(variant_selector, alt.value(50), alt.value(20)),
                strokeWidth=alt.condition(variant_selector, alt.value(2), alt.value(0)),
            )
        )

    combined_chart_total = alt.vconcat(
        combined_chart1,
        combined_chart2,
        base3,
        title=alt.Title(
            "Antibody Escape versus Binding",
            subtitle="Colored by Epitope. Hover over points to see the same sites",
        ),
    ).add_params(
        variant_selector
    )  
    return combined_chart_total


tmp_img_test = plot_escape_vs_binding(new_merged_df)
tmp_img_test.display()
if mab_line_escape_plot is not None:
    tmp_img_test.save(binding_vs_escape)

	site	wildtype	mutant	effect	effect_std	times_seen	n_selections
13	71	Q	P	-3.430	0.00000	6.714	7
34	72	N	P	-3.544	0.00000	7.857	7
39	72	N	V	-2.775	0.07748	7.571	7
55	73	Y	P	-3.356	0.16900	3.833	6
76	74	T	P	-3.194	0.12440	4.857	7
...	...	...	...	...	...	...	...
10768	597	I	S	-3.190	0.40170	3.286	7
10769	597	I	T	-3.494	0.02079	7.143	7
10772	597	I	Y	-2.367	0.66970	4.000	7
10774	598	P	C	-2.125	0.94490	5.143	7
10791	598	P	W	-3.169	0.00000	8.143	7

	site	wildtype	mutant	mutation	effect	escape_median	escape_std	times_seen_ab	show_site	ab
0	71	Q	D	Q71D	-0.4981	-0.003238	0.05961	3.333	False	HENV-103
1	71	Q	E	Q71E	0.3605	-0.029820	0.12310	3.333	False	HENV-103
2	71	Q	F	Q71F	-0.5317	0.012440	0.01263	2.333	False	HENV-103
3	71	Q	G	Q71G	-1.2470	0.040310	0.02698	3.333	False	HENV-103
4	71	Q	H	Q71H	-0.2558	0.014980	0.23130	2.667	False	HENV-103
...	...	...	...	...	...	...	...	...	...	...
6913	602	T	R	T602R	0.4772	-0.016640	0.00485	7.333	False	nAH1.3
6914	602	T	S	T602S	0.3906	0.161300	0.23030	3.667	False	nAH1.3
6915	602	T	V	T602V	0.3780	0.131000	0.07729	6.000	False	nAH1.3
6916	602	T	W	T602W	0.5438	0.071860	0.09132	6.333	False	nAH1.3
6917	602	T	Y	T602Y	0.4982	0.246200	0.09855	6.667	False	nAH1.3

	site	wildtype	mutant	mutation	effect	escape_median	escape_std	times_seen_ab	show_site	ab
906	154	K	I	K154I	-0.93860	0.5414	0.33560	5.333	True	HENV-103
912	154	K	S	K154S	0.23260	0.4880	0.31120	2.667	True	HENV-103
914	154	K	V	K154V	-0.77220	0.4362	0.32850	5.333	True	HENV-103
1180	176	E	F	E176F	0.24160	0.5403	0.34270	5.000	True	HENV-103
1185	176	E	L	E176L	-0.09272	0.4601	0.27780	5.000	True	HENV-103
...	...	...	...	...	...	...	...	...	...	...
5930	518	N	M	N518M	0.34070	0.9404	0.72310	5.667	True	nAH1.3
5931	518	N	P	N518P	-0.56450	0.9933	0.09195	5.333	True	nAH1.3
5933	518	N	R	N518R	0.44010	0.7831	0.24450	7.667	True	nAH1.3
5937	518	N	W	N518W	0.16300	0.8366	0.25700	6.000	True	nAH1.3
5938	518	N	Y	N518Y	-0.40690	1.5040	0.49130	5.333	True	nAH1.3

	site	wildtype	mutant	mutation	effect	escape_median	escape_std	times_seen_ab	show_site	ab	wt_codon	closest_mutant_codon	min_mutations
0	71	Q	D	Q71D	-0.4981	-0.003238	0.05961	3.333	False	HENV-103	CAA	GAC	2
1	71	Q	E	Q71E	0.3605	-0.029820	0.12310	3.333	False	HENV-103	CAA	GAA	1
2	71	Q	F	Q71F	-0.5317	0.012440	0.01263	2.333	False	HENV-103	CAA	None	3
3	71	Q	G	Q71G	-1.2470	0.040310	0.02698	3.333	False	HENV-103	CAA	GGA	2
4	71	Q	H	Q71H	-0.2558	0.014980	0.23130	2.667	False	HENV-103	CAA	CAC	1
...	...	...	...	...	...	...	...	...	...	...	...	...	...
6913	602	T	R	T602R	0.4772	-0.016640	0.00485	7.333	False	nAH1.3	ACA	AGA	1
6914	602	T	S	T602S	0.3906	0.161300	0.23030	3.667	False	nAH1.3	ACA	TCA	1
6915	602	T	V	T602V	0.3780	0.131000	0.07729	6.000	False	nAH1.3	ACA	GTA	2
6916	602	T	W	T602W	0.5438	0.071860	0.09132	6.333	False	nAH1.3	ACA	None	3
6917	602	T	Y	T602Y	0.4982	0.246200	0.09855	6.667	False	nAH1.3	ACA	None	3

This script analyzes filtered mAb escape data¶

For running interactively¶

Make logo plots¶

Filtering parameters¶

Read in filtered antibody escape files and combine.¶

Plot bubble chart showing mAb escape for individual mutants by functional score for both E2 or E3¶

Now summarize by number of mutations between wildtype and mutant codons¶

Line plots of escape¶

Now calculate atomic distances between escape sites and closest amino acid in heavy and light chains¶

Prepare dataframes for heatmaps¶

Make full antibody escape heatmaps¶

Now make heatmaps of antibody escape versus Ephrin Binding¶

Now show heatmap with nipah polymorphisms¶

Make plots comparing escape with binding to see if escape sites do so by increasing binding¶

	site	value	mutant	wildtype	effect
0	176	35.044434	distance		escape_median
1	177	31.866014	distance		escape_median
2	178	27.842815	distance		escape_median
3	179	28.777035	distance		escape_median
4	180	28.332012	distance		escape_median
...	...	...	...	...	...
423	599	30.802711	distance		escape_median
424	600	28.920950	distance		escape_median
425	601	27.248772	distance		escape_median
426	602	29.020868	distance		escape_median
427	603	27.945621	distance		escape_median

	site	mutant	wildtype	effect	value	ab
0	71	A	NaN	escape_median	NaN	m102.4
1	71	C	Q	escape_median	0.290000	m102.4
2	71	D	Q	escape_median	-0.021530	m102.4
3	71	E	Q	escape_median	0.017950	m102.4
4	71	F	Q	escape_median	0.004024	m102.4
...	...	...	...	...	...	...
13400	597	S	I	effect	-3.190000	HENV-103
13401	597	T	I	effect	-3.494000	HENV-103
13402	597	Y	I	effect	-2.367000	HENV-103
13403	598	C	P	effect	-2.125000	HENV-103
13404	598	W	P	effect	-3.169000	HENV-103

	site	effect	value	ab
0	71	escape_median	0.011995	m102.4
1	72	escape_median	0.037640	m102.4
2	73	escape_median	0.042650	m102.4
3	74	escape_median	-0.039695	m102.4
4	75	escape_median	-0.017860	m102.4
...	...	...	...	...
527	598	escape_median	0.158000	Ephrin-B2 binding
528	599	escape_median	-0.214000	Ephrin-B2 binding
529	600	escape_median	-0.037000	Ephrin-B2 binding
530	601	escape_median	0.240000	Ephrin-B2 binding
531	602	escape_median	-0.053500	Ephrin-B2 binding

	site	effect	value	ab
0	71	escape_median	0.42320	m102.4
1	72	escape_median	0.09214	m102.4
2	73	escape_median	0.33640	m102.4
3	74	escape_median	0.06910	m102.4
4	75	escape_median	0.11410	m102.4
...	...	...	...	...
25	478	median_escape	0.00000	NiV Polymorphism
26	481	median_escape	0.00000	NiV Polymorphism
27	498	median_escape	0.00000	NiV Polymorphism
28	502	median_escape	0.00000	NiV Polymorphism
29	545	median_escape	0.00000	NiV Polymorphism